After a lot of searching, I found that the ones in the old cacti-0.8.7d/rra directory were getting upgraded. I verified that the correct poller.php was running, and found that while it was reading its config from the cacti-0.8.7d-PA directory, it was writing its RRA output to the cacti-0.8.7d directory. I also just found that the log file is still being written to (and read from) the cacti-0.8.7b directory that I just upgraded from. God knows where that is coming from. The database, maybe?
Actually, I just looked and found that it's all coming from the database. Maybe there shouldn't be a full path like that in the database, but only a relative path? For now, I've workarounded by renaming my directories, and not deleting my old logfile, but this should probably be fixed.
Also, while researching this, I found that include/global.php contains the line:
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$config["cacti_version"] = "0.8.7c";